Starting phenix.real_space_refine on Fri Mar 15 03:03:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/03_2024/8sgw_40470_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/03_2024/8sgw_40470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/03_2024/8sgw_40470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/03_2024/8sgw_40470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/03_2024/8sgw_40470_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/03_2024/8sgw_40470_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 Cl 4 4.86 5 C 7028 2.51 5 N 1542 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D ASP 467": "OD1" <-> "OD2" Residue "D TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10414 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "C" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 452 Unusual residues: {' CL': 2, 'AV0': 1, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 452 Unusual residues: {' CL': 2, 'AV0': 1, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 6.66, per 1000 atoms: 0.64 Number of scatterers: 10414 At special positions: 0 Unit cell: (83.74, 121.9, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 36 16.00 P 6 15.00 O 1798 8.00 N 1542 7.00 C 7028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM10316 C18 DMU D 818 41.046 59.711 31.954 1.00 67.13 C !!! !!! HETATM 9864 C18 DMU C 818 41.691 61.056 31.971 1.00 66.94 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 2.1 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 2 sheets defined 63.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 80 through 108 removed outlier: 4.277A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 Proline residue: C 123 - end of helix removed outlier: 4.053A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 Processing helix chain 'C' and resid 158 through 161 No H-bonds generated for 'chain 'C' and resid 158 through 161' Processing helix chain 'C' and resid 178 through 205 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 217 through 240 Processing helix chain 'C' and resid 252 through 266 removed outlier: 5.481A pdb=" N GLY C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 291 Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'C' and resid 319 through 322 No H-bonds generated for 'chain 'C' and resid 319 through 322' Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.778A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 375 removed outlier: 3.778A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 397 Processing helix chain 'C' and resid 407 through 415 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 447 through 474 removed outlier: 4.252A pdb=" N LYS C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N MET C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL C 465 " --> pdb=" O MET C 461 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N CYS C 466 " --> pdb=" O PHE C 462 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) Proline residue: C 469 - end of helix Processing helix chain 'C' and resid 476 through 490 Processing helix chain 'C' and resid 494 through 514 Processing helix chain 'C' and resid 533 through 536 No H-bonds generated for 'chain 'C' and resid 533 through 536' Processing helix chain 'C' and resid 556 through 570 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.734A pdb=" N ILE C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 705 Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 80 through 108 removed outlier: 4.277A pdb=" N LEU D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 130 Proline residue: D 123 - end of helix removed outlier: 4.058A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 155 Processing helix chain 'D' and resid 158 through 161 No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 178 through 205 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 217 through 240 Processing helix chain 'D' and resid 252 through 266 removed outlier: 5.483A pdb=" N GLY D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 291 Processing helix chain 'D' and resid 302 through 317 Processing helix chain 'D' and resid 319 through 322 No H-bonds generated for 'chain 'D' and resid 319 through 322' Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.771A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 375 removed outlier: 3.760A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 397 Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 447 through 474 removed outlier: 4.252A pdb=" N LYS D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N MET D 461 " --> pdb=" O ASN D 457 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL D 465 " --> pdb=" O MET D 461 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N CYS D 466 " --> pdb=" O PHE D 462 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Proline residue: D 469 - end of helix Processing helix chain 'D' and resid 476 through 490 Processing helix chain 'D' and resid 494 through 514 Processing helix chain 'D' and resid 533 through 536 No H-bonds generated for 'chain 'D' and resid 533 through 536' Processing helix chain 'D' and resid 556 through 570 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 670 through 686 removed outlier: 3.734A pdb=" N ILE D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 705 Processing helix chain 'D' and resid 724 through 730 Processing sheet with id= A, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.129A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.665A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER C 657 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU C 548 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 659 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE C 550 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP C 661 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS C 689 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU C 660 " --> pdb=" O HIS C 689 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR C 691 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.129A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.663A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER D 657 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU D 548 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 659 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE D 550 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP D 661 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N HIS D 689 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU D 660 " --> pdb=" O HIS D 689 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 691 " --> pdb=" O LEU D 660 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1572 1.32 - 1.45: 2604 1.45 - 1.57: 6390 1.57 - 1.69: 12 1.69 - 1.81: 56 Bond restraints: 10634 Sorted by residual: bond pdb=" O2 LBN D 809 " pdb=" P1 LBN D 809 " ideal model delta sigma weight residual 1.650 1.595 0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O2 LBN C 807 " pdb=" P1 LBN C 807 " ideal model delta sigma weight residual 1.650 1.595 0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" O2 LBN D 806 " pdb=" P1 LBN D 806 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" O2 LBN D 807 " pdb=" P1 LBN D 807 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" O2 LBN C 809 " pdb=" P1 LBN C 809 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.16e+00 ... (remaining 10629 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.82: 252 105.82 - 112.87: 6022 112.87 - 119.91: 3569 119.91 - 126.96: 4485 126.96 - 134.00: 86 Bond angle restraints: 14414 Sorted by residual: angle pdb=" C ILE C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ILE D 491 " pdb=" N LEU D 492 " pdb=" CA LEU D 492 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.63e+01 angle pdb=" O1 LBN C 809 " pdb=" P1 LBN C 809 " pdb=" O2 LBN C 809 " ideal model delta sigma weight residual 93.45 104.00 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O1 LBN C 807 " pdb=" P1 LBN C 807 " pdb=" O2 LBN C 807 " ideal model delta sigma weight residual 93.45 103.99 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O1 LBN D 809 " pdb=" P1 LBN D 809 " pdb=" O2 LBN D 809 " ideal model delta sigma weight residual 93.45 103.97 -10.52 3.00e+00 1.11e-01 1.23e+01 ... (remaining 14409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 6850 33.37 - 66.75: 209 66.75 - 100.12: 43 100.12 - 133.50: 66 133.50 - 166.87: 10 Dihedral angle restraints: 7178 sinusoidal: 3628 harmonic: 3550 Sorted by residual: dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N HIS C 723 " pdb=" CA HIS C 723 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA VAL D 722 " pdb=" C VAL D 722 " pdb=" N HIS D 723 " pdb=" CA HIS D 723 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CBS AV0 D 819 " pdb=" C1 AV0 D 819 " pdb=" O1 AV0 D 819 " pdb=" O5 AV0 D 819 " ideal model delta sinusoidal sigma weight residual 85.89 -80.98 166.87 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 7175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 1756 0.988 - 1.976: 0 1.976 - 2.965: 0 2.965 - 3.953: 0 3.953 - 4.941: 4 Chirality restraints: 1760 Sorted by residual: chirality pdb=" C2 LBN D 806 " pdb=" C1 LBN D 806 " pdb=" C3 LBN D 806 " pdb=" O7 LBN D 806 " both_signs ideal model delta sigma weight residual False -2.36 2.58 -4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C2 LBN C 806 " pdb=" C1 LBN C 806 " pdb=" C3 LBN C 806 " pdb=" O7 LBN C 806 " both_signs ideal model delta sigma weight residual False -2.36 2.58 -4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C2 LBN C 809 " pdb=" C1 LBN C 809 " pdb=" C3 LBN C 809 " pdb=" O7 LBN C 809 " both_signs ideal model delta sigma weight residual False -2.36 2.50 -4.86 2.00e-01 2.50e+01 5.91e+02 ... (remaining 1757 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 809 " 0.235 2.00e-02 2.50e+03 2.37e-01 5.62e+02 pdb=" C42 LBN D 809 " -0.231 2.00e-02 2.50e+03 pdb=" C5 LBN D 809 " -0.243 2.00e-02 2.50e+03 pdb=" C8 LBN D 809 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 809 " -0.217 2.00e-02 2.50e+03 2.17e-01 4.71e+02 pdb=" C42 LBN C 809 " 0.217 2.00e-02 2.50e+03 pdb=" C5 LBN C 809 " 0.217 2.00e-02 2.50e+03 pdb=" C8 LBN C 809 " -0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 806 " 0.094 2.00e-02 2.50e+03 2.05e-01 4.22e+02 pdb=" C42 LBN C 806 " -0.274 2.00e-02 2.50e+03 pdb=" C5 LBN C 806 " 0.275 2.00e-02 2.50e+03 pdb=" C8 LBN C 806 " -0.095 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 3 2.17 - 2.86: 3485 2.86 - 3.54: 15419 3.54 - 4.22: 24793 4.22 - 4.90: 43805 Nonbonded interactions: 87505 Sorted by model distance: nonbonded pdb=" C18 DMU C 818 " pdb=" C18 DMU D 818 " model vdw 1.492 3.840 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.135 2.520 nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.136 2.520 nonbonded pdb=" OH TYR D 78 " pdb=" OD2 ASP D 87 " model vdw 2.208 2.440 nonbonded pdb=" OH TYR C 78 " pdb=" OD2 ASP C 87 " model vdw 2.209 2.440 ... (remaining 87500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.250 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.780 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10634 Z= 0.263 Angle : 0.688 10.547 14414 Z= 0.328 Chirality : 0.238 4.941 1760 Planarity : 0.012 0.237 1640 Dihedral : 21.885 166.873 4890 Min Nonbonded Distance : 1.492 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1210 helix: 1.58 (0.19), residues: 804 sheet: -0.07 (0.57), residues: 54 loop : -1.82 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.003 0.001 HIS C 656 PHE 0.017 0.001 PHE D 141 TYR 0.020 0.002 TYR D 27 ARG 0.003 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.305 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 167 average time/residue: 0.9946 time to fit residues: 181.6220 Evaluate side-chains 125 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 250 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN C 705 GLN D 324 ASN D 705 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10634 Z= 0.193 Angle : 0.674 11.276 14414 Z= 0.311 Chirality : 0.044 0.252 1760 Planarity : 0.004 0.068 1640 Dihedral : 19.029 161.607 2744 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.63 % Allowed : 10.61 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1210 helix: 1.61 (0.19), residues: 806 sheet: 0.42 (0.58), residues: 50 loop : -1.82 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 74 HIS 0.003 0.001 HIS D 656 PHE 0.017 0.001 PHE D 141 TYR 0.011 0.001 TYR C 371 ARG 0.003 0.000 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.129 Fit side-chains REVERT: C 27 TYR cc_start: 0.7206 (m-80) cc_final: 0.6921 (m-80) REVERT: C 84 LEU cc_start: 0.8224 (mm) cc_final: 0.7968 (mt) REVERT: C 678 MET cc_start: 0.7191 (mmt) cc_final: 0.6958 (mmt) REVERT: C 682 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7097 (mt-10) REVERT: C 684 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: D 27 TYR cc_start: 0.7203 (m-80) cc_final: 0.6919 (m-80) REVERT: D 84 LEU cc_start: 0.8226 (mm) cc_final: 0.7970 (mt) REVERT: D 678 MET cc_start: 0.7192 (mmt) cc_final: 0.6957 (mmt) REVERT: D 682 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7101 (mt-10) REVERT: D 684 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7522 (tt0) outliers start: 17 outliers final: 12 residues processed: 146 average time/residue: 0.8694 time to fit residues: 141.0691 Evaluate side-chains 137 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 324 ASN D 33 GLN D 289 ASN D 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10634 Z= 0.201 Angle : 0.612 9.020 14414 Z= 0.297 Chirality : 0.045 0.269 1760 Planarity : 0.004 0.070 1640 Dihedral : 17.380 163.709 2742 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.91 % Allowed : 13.19 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1210 helix: 1.61 (0.19), residues: 810 sheet: 0.42 (0.58), residues: 50 loop : -1.84 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 PHE 0.017 0.001 PHE D 141 TYR 0.012 0.001 TYR D 371 ARG 0.003 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.072 Fit side-chains REVERT: C 27 TYR cc_start: 0.7283 (m-80) cc_final: 0.6820 (m-80) REVERT: C 678 MET cc_start: 0.7109 (mmt) cc_final: 0.6863 (mmt) REVERT: C 682 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7242 (mt-10) REVERT: D 27 TYR cc_start: 0.7285 (m-80) cc_final: 0.6822 (m-80) REVERT: D 678 MET cc_start: 0.7109 (mmt) cc_final: 0.6862 (mmt) REVERT: D 682 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7245 (mt-10) outliers start: 20 outliers final: 11 residues processed: 138 average time/residue: 0.8351 time to fit residues: 128.3847 Evaluate side-chains 129 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN D 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10634 Z= 0.264 Angle : 0.648 10.201 14414 Z= 0.317 Chirality : 0.047 0.335 1760 Planarity : 0.005 0.073 1640 Dihedral : 16.582 167.107 2742 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 3.06 % Allowed : 13.19 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1210 helix: 1.49 (0.18), residues: 808 sheet: 0.43 (0.59), residues: 50 loop : -1.75 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 74 HIS 0.003 0.001 HIS D 698 PHE 0.018 0.002 PHE C 401 TYR 0.014 0.002 TYR C 371 ARG 0.003 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.195 Fit side-chains REVERT: C 27 TYR cc_start: 0.7389 (m-80) cc_final: 0.6813 (m-80) REVERT: C 678 MET cc_start: 0.7098 (mmt) cc_final: 0.6844 (mpm) REVERT: C 684 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: D 27 TYR cc_start: 0.7392 (m-80) cc_final: 0.6814 (m-80) REVERT: D 678 MET cc_start: 0.7098 (mmt) cc_final: 0.6840 (mpm) REVERT: D 684 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7578 (tt0) outliers start: 32 outliers final: 16 residues processed: 145 average time/residue: 0.8305 time to fit residues: 133.9495 Evaluate side-chains 133 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN D 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10634 Z= 0.198 Angle : 0.609 9.477 14414 Z= 0.299 Chirality : 0.045 0.331 1760 Planarity : 0.004 0.076 1640 Dihedral : 15.609 167.711 2742 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.54 % Allowed : 13.58 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1210 helix: 1.53 (0.18), residues: 814 sheet: 0.25 (0.58), residues: 50 loop : -1.66 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 PHE 0.016 0.001 PHE C 141 TYR 0.014 0.001 TYR D 556 ARG 0.002 0.000 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7373 (m-80) cc_final: 0.6612 (m-80) REVERT: C 81 LYS cc_start: 0.7702 (mmpt) cc_final: 0.7015 (mmtm) REVERT: C 684 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: D 27 TYR cc_start: 0.7374 (m-80) cc_final: 0.6612 (m-80) REVERT: D 81 LYS cc_start: 0.7692 (mmpt) cc_final: 0.7008 (mmtm) REVERT: D 684 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7517 (tt0) outliers start: 37 outliers final: 23 residues processed: 156 average time/residue: 0.7918 time to fit residues: 138.4982 Evaluate side-chains 147 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN C 324 ASN D 289 ASN D 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10634 Z= 0.229 Angle : 0.643 9.978 14414 Z= 0.313 Chirality : 0.046 0.321 1760 Planarity : 0.005 0.076 1640 Dihedral : 15.208 167.757 2742 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.44 % Allowed : 13.86 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1210 helix: 1.47 (0.18), residues: 812 sheet: 0.20 (0.58), residues: 50 loop : -1.68 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 PHE 0.018 0.002 PHE C 141 TYR 0.013 0.002 TYR D 371 ARG 0.003 0.000 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.214 Fit side-chains REVERT: C 27 TYR cc_start: 0.7393 (m-80) cc_final: 0.6670 (m-80) REVERT: C 81 LYS cc_start: 0.7719 (mmpt) cc_final: 0.7056 (mmtm) REVERT: C 682 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7231 (mt-10) REVERT: C 684 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: D 27 TYR cc_start: 0.7393 (m-80) cc_final: 0.6670 (m-80) REVERT: D 81 LYS cc_start: 0.7711 (mmpt) cc_final: 0.7048 (mmtm) REVERT: D 682 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7234 (mt-10) REVERT: D 684 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7498 (tt0) outliers start: 36 outliers final: 22 residues processed: 149 average time/residue: 0.7997 time to fit residues: 133.4266 Evaluate side-chains 143 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN D 289 ASN D 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10634 Z= 0.164 Angle : 0.605 9.949 14414 Z= 0.292 Chirality : 0.044 0.317 1760 Planarity : 0.004 0.074 1640 Dihedral : 14.244 166.315 2742 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.58 % Allowed : 15.20 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1210 helix: 1.64 (0.19), residues: 814 sheet: 0.17 (0.57), residues: 50 loop : -1.69 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 PHE 0.015 0.001 PHE D 141 TYR 0.011 0.001 TYR D 556 ARG 0.003 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.182 Fit side-chains REVERT: C 27 TYR cc_start: 0.7397 (m-80) cc_final: 0.6640 (m-80) REVERT: C 81 LYS cc_start: 0.7715 (mmpt) cc_final: 0.7006 (mmtm) REVERT: C 682 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7204 (mt-10) REVERT: C 684 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: D 27 TYR cc_start: 0.7402 (m-80) cc_final: 0.6643 (m-80) REVERT: D 81 LYS cc_start: 0.7707 (mmpt) cc_final: 0.6998 (mmtm) REVERT: D 682 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 684 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7503 (tt0) outliers start: 27 outliers final: 18 residues processed: 149 average time/residue: 0.8024 time to fit residues: 133.6936 Evaluate side-chains 145 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10634 Z= 0.231 Angle : 0.648 10.235 14414 Z= 0.317 Chirality : 0.046 0.345 1760 Planarity : 0.005 0.075 1640 Dihedral : 14.135 165.992 2742 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.87 % Allowed : 15.68 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1210 helix: 1.58 (0.18), residues: 812 sheet: 0.25 (0.58), residues: 50 loop : -1.67 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 PHE 0.018 0.002 PHE C 141 TYR 0.017 0.002 TYR C 315 ARG 0.003 0.000 ARG D 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 1.169 Fit side-chains REVERT: C 27 TYR cc_start: 0.7422 (m-80) cc_final: 0.6695 (m-80) REVERT: C 81 LYS cc_start: 0.7702 (mmpt) cc_final: 0.6977 (mmtm) REVERT: C 682 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7218 (mt-10) REVERT: C 684 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: D 27 TYR cc_start: 0.7425 (m-80) cc_final: 0.6696 (m-80) REVERT: D 81 LYS cc_start: 0.7712 (mmpt) cc_final: 0.7009 (mmtm) REVERT: D 682 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7221 (mt-10) REVERT: D 684 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7506 (tt0) outliers start: 30 outliers final: 19 residues processed: 140 average time/residue: 0.7877 time to fit residues: 123.1843 Evaluate side-chains 139 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10634 Z= 0.170 Angle : 0.607 9.622 14414 Z= 0.298 Chirality : 0.044 0.354 1760 Planarity : 0.004 0.073 1640 Dihedral : 13.549 163.807 2742 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.20 % Allowed : 16.16 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1210 helix: 1.70 (0.19), residues: 814 sheet: 0.17 (0.57), residues: 50 loop : -1.65 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 PHE 0.016 0.001 PHE C 141 TYR 0.019 0.001 TYR D 315 ARG 0.003 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.301 Fit side-chains REVERT: C 27 TYR cc_start: 0.7437 (m-80) cc_final: 0.6662 (m-80) REVERT: C 81 LYS cc_start: 0.7657 (mmpt) cc_final: 0.7017 (mmtm) REVERT: C 682 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 684 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: D 27 TYR cc_start: 0.7444 (m-80) cc_final: 0.6665 (m-80) REVERT: D 81 LYS cc_start: 0.7656 (mmpt) cc_final: 0.6917 (mmtm) REVERT: D 682 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7228 (mt-10) REVERT: D 684 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7512 (tt0) outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 0.8249 time to fit residues: 128.7059 Evaluate side-chains 144 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10634 Z= 0.172 Angle : 0.609 10.258 14414 Z= 0.299 Chirality : 0.044 0.321 1760 Planarity : 0.004 0.072 1640 Dihedral : 13.162 161.271 2742 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.20 % Allowed : 16.25 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1210 helix: 1.78 (0.19), residues: 808 sheet: 0.32 (0.59), residues: 50 loop : -1.66 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 PHE 0.017 0.001 PHE C 141 TYR 0.009 0.001 TYR C 556 ARG 0.003 0.000 ARG D 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.094 Fit side-chains REVERT: C 27 TYR cc_start: 0.7383 (m-80) cc_final: 0.6735 (m-80) REVERT: C 682 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 684 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: D 27 TYR cc_start: 0.7387 (m-80) cc_final: 0.6735 (m-80) REVERT: D 81 LYS cc_start: 0.7653 (mmpt) cc_final: 0.7008 (mmtm) REVERT: D 682 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7235 (mt-10) REVERT: D 684 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7474 (tt0) outliers start: 23 outliers final: 15 residues processed: 143 average time/residue: 0.8350 time to fit residues: 133.4422 Evaluate side-chains 138 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.168049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133831 restraints weight = 12703.762| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.03 r_work: 0.3508 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10634 Z= 0.227 Angle : 0.649 10.413 14414 Z= 0.318 Chirality : 0.045 0.293 1760 Planarity : 0.005 0.074 1640 Dihedral : 13.127 159.813 2742 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.10 % Allowed : 16.06 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1210 helix: 1.61 (0.18), residues: 812 sheet: 0.28 (0.58), residues: 50 loop : -1.71 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.003 0.001 HIS C 656 PHE 0.018 0.002 PHE C 121 TYR 0.017 0.002 TYR D 315 ARG 0.003 0.000 ARG D 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3228.79 seconds wall clock time: 58 minutes 19.64 seconds (3499.64 seconds total)